Making genotyping cheaper and easier

Background
The opportunity to capture the full spectrum of genetic variants in any given species is crucial, as this allows accurate classification of individuals and the more accurate linkage of causal variants to phenotypes. There are now a plethora of tools and techniques that allow differential profiling of variant types, from single nucleotide polymorphisms, to DNA base modifications. The challenge is to develop approaches that are easier to execute and analyse.

Objectives
This studentship will aim to develop both laboratory and bioinformatics techniques to capture the full spectrum of genetic variants using a variety of biological models with modifications of agronomic importance that require the development of specific tests to study non-standard genetic modifications.

Approaches
The research work will be divided into upto four workpackages (WPs), each with clear deliverables. These may include:
WP1: SNP panel construction- work to identify a low cost method for SNP evaluation using single molecule sequencing
WP2: Epi-allele identification using single molecule sequencing- using Phytophthora fragariae as a model of epiallelic variation
WP3: Structural variant tracking- using Fusarium formae specialis structural rearrangements to identify dynamic genomic rearrangements
WP4: k-mer and signature based identification- reference free approaches of tracking allelic variation using single molecule sequencing.
Benefit to the industry
The research outcome from this work will enable the development of novel genotyping technologies that can be used in breeding, varietal characterization and molecular diagnostics.